The ability to determine nucleic acid sequences is important for applications such as understanding the function and control of genes, or for applying many of the basic techniques of molecular biology. Sequencing by hybridization (SBH) is an approach to DNA sequencing that has been recently developed. In sequencing by hybridization, a large set of single-stranded fragments or probes are attached to a substrate. A solution of labeled single-stranded target DNA fragments is exposed to the substrate. These fragments hybridize with the complementary fragments on the substrate, and the hybridized fragments can be identified using a detector or a fluorescent/phosphorescent dye, depending on the selected label. The target DNA is then sequenced based on the pattern of hybridization of the fragments with the chip. However, current SBH techniques have several problems that limit their application, such as requiring relatively large quantities of reagents, or having relatively small throughput.